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The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental…
We present a quantitative benchmark of multiscale models for dendritic growth simulations. We focus on approaches based on phase-field, dendritic needle network, and grain envelope dynamics. As a first step, we focus on isothermal growth of…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
It is widely believed that the perceptual system of an organism is optimized for the properties of the environment to which it is exposed. A specific instance of this principle known as the Infomax principle holds that the purpose of early…
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages like facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
Cancer progression and monotonic accumulation models were developed to discover dependencies in the irreversible acquisition of binary traits from cross-sectional data. They have been used in computational oncology and virology but also in…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
We investigate the evolution of a population of non-interacting particles which undergo diffusion and multiplication. Diffusion is assumed to be homogeneous, while multiplication proceeds with different rates reflecting the distribution of…
Providing diagnostic feedback about growth is crucial to formative decisions such as targeted remedial instructions or interventions. This paper proposed a longitudinal higher-order diagnostic classification modeling approach for measuring…
The high energy consumption of electronic data processors, together with physical challenges limiting their further improvement, has triggered intensive interest in alternative computation paradigms. Here we focus on network-based…
Growth patterns of complex systems predict how they change in sizes, numbers, masses, etc. Understanding growth is important, especially for many biological, ecological, urban, and socioeconomic systems. One noteworthy growth behavior is…
A mathematical model for emerging contaminants sorption in multispecies biofilms, based on a continuum approach and mass conservation principles is presented. Diffusion of contaminants within the biofilm is described using a…
Quantitative assessment of the growth of biological organisms has produced many mathematical equations. Many efforts have been given on statistical identification of the correct growth model from experimental data. Every growth equation is…
We synthesise traditional unstructured food webs, allometric body size scaling, trait-based modelling, and physiologically structured modelling to provide a novel and ecologically relevant tool for size-structured food webs. The framework…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
Irrigation decision systems and water need models have been important research topics in agriculture since 90s. They improve the efficiency of crop yields, provide an appropriate use of water on the earth and so, prevent the water scarcity…
In this work we study the interplay between the dynamics of a model of diffusion governed by a mechanism of imitation and its underlying structure. The dynamics of the model can be quantified by a macroscopic observable which permits the…
Growth mixture models are an important tool for detecting group structure in repeated measures data. Unlike traditional clustering methods, they explicitly model the repeat measurements on observations, and the statistical framework they…